The higher temperature is something to be careful with. Unless there is any particular reason to increase it, one should stick to the default (or lower).
In some cases, the default temperature does however cause problems for the convergence, because it gives a relatively sharp Fermi function. This can make the SCF loop take a lot of steps, or it doesn't converge at all. In this case, you can smooth the Fermi function by increasing the temperature to 1000-15000 K, and often this will mean convergence is much better.
However, doing so actually influences the results, because you smear out the transport properties over a much larger energy interval. Therefore, the proper approach in this case is to take the results (i.e., the converged density matrix, contained in the NetCDF checkpoint file) obtained from the high-temperature calculation, and use those as a starting point for a low-temperature calculation, and in this way "anneal" the system. Usually the low-temperature calculation is able to converge once it has a reasonable starting guess, as provided this way.
So, why the higher temperature in the example in the manual? Well, basically, it was chosen to make the calculation converge fast and easily. It's not a really physically proper system anyway, and the focus of that chapter is how to relax a two-probe system, so the parameters were chosen as conveniently as possible...